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Protein

Lysine-specific demethylase 4B

Gene

KDM4B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. Demethylation of Lys residue generates formaldehyde and succinate.1 Publication

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei133Alpha-ketoglutarateBy similarity1
Metal bindingi189Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi191Iron; catalyticPROSITE-ProRule annotation1
Binding sitei199Alpha-ketoglutarateBy similarity1
Binding sitei207Alpha-ketoglutarateBy similarity1
Metal bindingi235ZincBy similarity1
Metal bindingi241ZincBy similarity1
Metal bindingi277Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi307ZincBy similarity1
Metal bindingi309ZincBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri731 – 789PHD-type 1Add BLAST59
Zinc fingeri794 – 827C2HC pre-PHD-typePROSITE-ProRule annotationAdd BLAST34
Zinc fingeri850 – 907PHD-type 2PROSITE-ProRule annotationAdd BLAST58

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000127663-MONOMER.
BRENDAi1.14.11.B1. 2681.
ReactomeiR-HSA-3214842. HDMs demethylate histones.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 4B (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 3B
Jumonji domain-containing protein 2B
Gene namesi
Name:KDM4B
Synonyms:JHDM3B, JMJD2B, KIAA0876
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:29136. KDM4B.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi23030.
OpenTargetsiENSG00000127663.
PharmGKBiPA164721452.

Chemistry databases

ChEMBLiCHEMBL3313832.

Polymorphism and mutation databases

BioMutaiKDM4B.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001831751 – 1096Lysine-specific demethylase 4BAdd BLAST1096

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei566PhosphoserineCombined sources1
Modified residuei602N6-acetyllysineCombined sources1
Modified residuei1065PhosphothreonineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiO94953.
MaxQBiO94953.
PaxDbiO94953.
PeptideAtlasiO94953.
PRIDEiO94953.

PTM databases

iPTMnetiO94953.
PhosphoSitePlusiO94953.

Expressioni

Gene expression databases

BgeeiENSG00000127663.
CleanExiHS_JMJD2B.
ExpressionAtlasiO94953. baseline and differential.

Organism-specific databases

HPAiHPA062872.

Interactioni

Protein-protein interaction databases

BioGridi116669. 28 interactors.
DIPiDIP-47283N.
IntActiO94953. 6 interactors.
MINTiMINT-1427202.
STRINGi9606.ENSP00000159111.

Chemistry databases

BindingDBiO94953.

Structurei

Secondary structure

11096
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi22 – 25Combined sources4
Helixi28 – 37Combined sources10
Helixi40 – 43Combined sources4
Beta strandi44 – 48Combined sources5
Helixi63 – 65Combined sources3
Beta strandi67 – 70Combined sources4
Beta strandi72 – 79Combined sources8
Beta strandi82 – 89Combined sources8
Helixi95 – 103Combined sources9
Turni105 – 107Combined sources3
Helixi115 – 125Combined sources11
Beta strandi132 – 138Combined sources7
Helixi157 – 159Combined sources3
Helixi160 – 165Combined sources6
Turni170 – 172Combined sources3
Beta strandi176 – 180Combined sources5
Beta strandi185 – 189Combined sources5
Helixi192 – 194Combined sources3
Beta strandi196 – 205Combined sources10
Beta strandi207 – 212Combined sources6
Helixi214 – 216Combined sources3
Helixi217 – 227Combined sources11
Helixi229 – 234Combined sources6
Helixi238 – 241Combined sources4
Beta strandi244 – 246Combined sources3
Helixi248 – 253Combined sources6
Beta strandi259 – 263Combined sources5
Beta strandi268 – 271Combined sources4
Beta strandi276 – 281Combined sources6
Beta strandi283 – 292Combined sources10
Helixi295 – 297Combined sources3
Helixi298 – 303Combined sources6
Helixi319 – 325Combined sources7
Helixi327 – 334Combined sources8
Beta strandi924 – 928Combined sources5
Beta strandi934 – 951Combined sources18
Beta strandi957 – 961Combined sources5
Helixi963 – 965Combined sources3
Beta strandi966 – 969Combined sources4
Helixi971 – 974Combined sources4
Beta strandi982 – 986Combined sources5
Beta strandi992 – 1010Combined sources19
Beta strandi1015 – 1019Combined sources5
Helixi1020 – 1022Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LXLX-ray1.87A1-348[»]
4UC4X-ray2.56A/B917-1031[»]
ProteinModelPortaliO94953.
SMRiO94953.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini15 – 57JmjNPROSITE-ProRule annotationAdd BLAST43
Domaini146 – 309JmjCPROSITE-ProRule annotationAdd BLAST164
Domaini917 – 974Tudor 1Add BLAST58
Domaini975 – 1031Tudor 2Add BLAST57

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi463 – 535Pro-richAdd BLAST73

Domaini

The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails (By similarity).By similarity

Sequence similaritiesi

Belongs to the JHDM3 histone demethylase family.Curated
Contains 1 C2HC pre-PHD-type zinc finger.PROSITE-ProRule annotation
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation
Contains 2 Tudor domains.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri731 – 789PHD-type 1Add BLAST59
Zinc fingeri794 – 827C2HC pre-PHD-typePROSITE-ProRule annotationAdd BLAST34
Zinc fingeri850 – 907PHD-type 2PROSITE-ProRule annotationAdd BLAST58

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IT40. Eukaryota.
COG5141. LUCA.
GeneTreeiENSGT00530000063342.
InParanoidiO94953.
KOiK06709.
PhylomeDBiO94953.
TreeFamiTF106449.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51805. EPHD. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O94953-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGSEDHGAQN PSCKIMTFRP TMEEFKDFNK YVAYIESQGA HRAGLAKIIP
60 70 80 90 100
PKEWKPRQTY DDIDDVVIPA PIQQVVTGQS GLFTQYNIQK KAMTVGEYRR
110 120 130 140 150
LANSEKYCTP RHQDFDDLER KYWKNLTFVS PIYGADISGS LYDDDVAQWN
160 170 180 190 200
IGSLRTILDM VERECGTIIE GVNTPYLYFG MWKTTFAWHT EDMDLYSINY
210 220 230 240 250
LHFGEPKSWY AIPPEHGKRL ERLAIGFFPG SSQGCDAFLR HKMTLISPII
260 270 280 290 300
LKKYGIPFSR ITQEAGEFMI TFPYGYHAGF NHGFNCAEST NFATLRWIDY
310 320 330 340 350
GKVATQCTCR KDMVKISMDV FVRILQPERY ELWKQGKDLT VLDHTRPTAL
360 370 380 390 400
TSPELSSWSA SRASLKAKLL RRSHRKRSQP KKPKPEDPKF PGEGTAGAAL
410 420 430 440 450
LEEAGGSVKE EAGPEVDPEE EEEEPQPLPH GREAEGAEED GRGKLRPTKA
460 470 480 490 500
KSERKKKSFG LLPPQLPPPP AHFPSEEALW LPSPLEPPVL GPGPAAMEES
510 520 530 540 550
PLPAPLNVVP PEVPSEELEA KPRPIIPMLY VVPRPGKAAF NQEHVSCQQA
560 570 580 590 600
FEHFAQKGPT WKEPVSPMEL TGPEDGAASS GAGRMETKAR AGEGQAPSTF
610 620 630 640 650
SKLKMEIKKS RRHPLGRPPT RSPLSVVKQE ASSDEEASPF SGEEDVSDPD
660 670 680 690 700
ALRPLLSLQW KNRAASFQAE RKFNAAAART EPYCAICTLF YPYCQALQTE
710 720 730 740 750
KEAPIASLGK GCPATLPSKS RQKTRPLIPE MCFTSGGENT EPLPANSYIG
760 770 780 790 800
DDGTSPLIAC GKCCLQVHAS CYGIRPELVN EGWTCSRCAA HAWTAECCLC
810 820 830 840 850
NLRGGALQMT TDRRWIHVIC AIAVPEARFL NVIERHPVDI SAIPEQRWKL
860 870 880 890 900
KCVYCRKRMK KVSGACIQCS YEHCSTSFHV TCAHAAGVLM EPDDWPYVVS
910 920 930 940 950
ITCLKHKSGG HAVQLLRAVS LGQVVITKNR NGLYYRCRVI GAASQTCYEV
960 970 980 990 1000
NFDDGSYSDN LYPESITSRD CVQLGPPSEG ELVELRWTDG NLYKAKFISS
1010 1020 1030 1040 1050
VTSHIYQVEF EDGSQLTVKR GDIFTLEEEL PKRVRSRLSL STGAPQEPAF
1060 1070 1080 1090
SGEEAKAAKR PRVGTPLATE DSGRSQDYVA FVESLLQVQG RPGAPF
Length:1,096
Mass (Da):121,897
Last modified:March 20, 2007 - v4
Checksum:i300D5CD6F2DD4330
GO
Isoform 2 (identifier: O94953-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     373-448: SHRKRSQPKK...EDGRGKLRPT → TPPCVSPHRP...LRMATQDPCR
     449-1096: Missing.

Note: No experimental confirmation available.
Show »
Length:448
Mass (Da):50,582
Checksum:i84E9B0DEEF9C84F9
GO

Sequence cautioni

The sequence AAC33799 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence BAA74899 differs from that shown. Reason: Erroneous initiation.Curated

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02622329N → T.Corresponds to variant rs11667206dbSNPEnsembl.1
Natural variantiVAR_026224710K → E.4 PublicationsCorresponds to variant rs2620836dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_018307373 – 448SHRKR…KLRPT → TPPCVSPHRPSQPGIWCPPG GEAKASAASWLLTTRGHGDT EAGPGLGGDPLHAQSEGQAS CVSTSRLRMATQDPCR in isoform 2. 1 PublicationAdd BLAST76
Alternative sequenceiVSP_018308449 – 1096Missing in isoform 2. 1 PublicationAdd BLAST648

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB020683 mRNA. Translation: BAA74899.2. Different initiation.
AC005595 Genomic DNA. Translation: AAC33799.1. Sequence problems.
AC022517 Genomic DNA. Translation: AAF31271.1.
CH471139 Genomic DNA. Translation: EAW69181.1.
CH471139 Genomic DNA. Translation: EAW69183.1.
BC063889 mRNA. Translation: AAH63889.1.
BC136611 mRNA. Translation: AAI36612.1.
AL133622 mRNA. Translation: CAB63748.2.
CCDSiCCDS12138.1. [O94953-1]
PIRiT43460.
RefSeqiNP_055830.1. NM_015015.2.
UniGeneiHs.654816.

Genome annotation databases

EnsembliENST00000381759; ENSP00000371178; ENSG00000127663. [O94953-2]
GeneIDi23030.
KEGGihsa:23030.
UCSCiuc002mbq.5. human. [O94953-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB020683 mRNA. Translation: BAA74899.2. Different initiation.
AC005595 Genomic DNA. Translation: AAC33799.1. Sequence problems.
AC022517 Genomic DNA. Translation: AAF31271.1.
CH471139 Genomic DNA. Translation: EAW69181.1.
CH471139 Genomic DNA. Translation: EAW69183.1.
BC063889 mRNA. Translation: AAH63889.1.
BC136611 mRNA. Translation: AAI36612.1.
AL133622 mRNA. Translation: CAB63748.2.
CCDSiCCDS12138.1. [O94953-1]
PIRiT43460.
RefSeqiNP_055830.1. NM_015015.2.
UniGeneiHs.654816.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4LXLX-ray1.87A1-348[»]
4UC4X-ray2.56A/B917-1031[»]
ProteinModelPortaliO94953.
SMRiO94953.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116669. 28 interactors.
DIPiDIP-47283N.
IntActiO94953. 6 interactors.
MINTiMINT-1427202.
STRINGi9606.ENSP00000159111.

Chemistry databases

BindingDBiO94953.
ChEMBLiCHEMBL3313832.

PTM databases

iPTMnetiO94953.
PhosphoSitePlusiO94953.

Polymorphism and mutation databases

BioMutaiKDM4B.

Proteomic databases

EPDiO94953.
MaxQBiO94953.
PaxDbiO94953.
PeptideAtlasiO94953.
PRIDEiO94953.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000381759; ENSP00000371178; ENSG00000127663. [O94953-2]
GeneIDi23030.
KEGGihsa:23030.
UCSCiuc002mbq.5. human. [O94953-1]

Organism-specific databases

CTDi23030.
DisGeNETi23030.
GeneCardsiKDM4B.
HGNCiHGNC:29136. KDM4B.
HPAiHPA062872.
MIMi609765. gene.
neXtProtiNX_O94953.
OpenTargetsiENSG00000127663.
PharmGKBiPA164721452.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410IT40. Eukaryota.
COG5141. LUCA.
GeneTreeiENSGT00530000063342.
InParanoidiO94953.
KOiK06709.
PhylomeDBiO94953.
TreeFamiTF106449.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000127663-MONOMER.
BRENDAi1.14.11.B1. 2681.
ReactomeiR-HSA-3214842. HDMs demethylate histones.
R-HSA-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.

Miscellaneous databases

ChiTaRSiKDM4B. human.
GeneWikiiJMJD2B.
GenomeRNAii23030.
PROiO94953.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000127663.
CleanExiHS_JMJD2B.
ExpressionAtlasiO94953. baseline and differential.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51805. EPHD. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiKDM4B_HUMAN
AccessioniPrimary (citable) accession number: O94953
Secondary accession number(s): B9EGN8
, D6W631, O75274, Q6P3R5, Q9P1V1, Q9UF40
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: March 20, 2007
Last modified: November 2, 2016
This is version 148 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.